mouse genome survey microarray  (Thermo Fisher)

Journal: PLoS ONE

Article Title: Estradiol Activates β-Catenin Dependent Transcription in Neurons

doi: 10.1371/journal.pone.0005153

Figure Lengend Snippet: Results of the Microarray analysis of gene transcription.

Article Snippet: Gene expression profiles were generated using Applied Biosystems Mouse Genome Survey Microarray.

Techniques: Microarray, Derivative Assay, Binding Assay, Sequencing

Journal: PLoS ONE

Article Title: Estradiol Activates β-Catenin Dependent Transcription in Neurons

doi: 10.1371/journal.pone.0005153

Figure Lengend Snippet: (A)- Gene expression profile in cDNA/N2a-m and Δ56LEF-1/N2a-m stables cell lines. The upper panel reflects the gene induction of some selected genes, in microarray analysis of RNA collected after a 45 min exposure to estradiol or Wnt3a to detect the early response. Data is expressed as log 2 R from cDNA/N2a-m cells, that we denoted as group A, and Δ56LEF-1/N2a-m cells, that we denoted as group B. The effect of the treatment was compared between the two stable cell lines (A vs B) (see “ ” for a more complete list of the annotated genes). As seen, in the panel we selected some “putative Wnt-regulated genes”, such as Tcf3 , Ccnd1 (cyclin D1), GSK3b , Myc and LEF-1 , to give some examples of the results in our arrays. We detected changes at the protein level only in Plg , although there were several genes whose expression varied. For example, the levels of plasminogen RNA were much higher in group B than group A (ratio AvsB≥1), and the expression of LEF-1 was higher in Δ56LEF-1 due to the mutant expression (ratio AvsB≤−1). The western blots below are verifications of these differences at the protein level. Among other proteins that did not change between the groups of cells were GSK3 β or myc (see western blots on the right). MMP-2 was tested although it did not display a change in its RNA levels and there was no difference in the total cell extracts. Interestingly, when conditioned medium was prepared, more pro-active MMP-2 (and less active protein) was seen in Δ56LEF-1 cells. [Gene_Symbol: Plg (plasminogen), Tcf3 , Ccnd1 (cyclin D1), GSK3b , Myc and LEF1 ]. (B)- Estradiol induction of N-cadherin and cyclin D2 may be affected by expression of the Δ56LEF-1 protein. Total cell extracts from cDNA/N2a-m cells (group A) and Δ56LEF-1/N2a-m cells (group B) were collected 24 h after estradiol or Wnt3a treatment to analyze several known Wnt or estrogen target genes. As seen in western blots, estradiol upregulated E-cadherin, N-cadherin and cyclin D2 expression in group A cells. N-cadherin and cyclin D2 were also upregulated by Wnt in group A cells. In contrast, E-cadherin expression was not Wnt responsive. The regulatory effects of estradiol on E-cadherin, N-cadherin and cyclin D2 expression were lost when Δ56LEF-1 is expressed, as seen in group B cells. In the case of E-cadherin, the loss of functional LEF-1, which acts as a known gene repressor, implies higher protein levels even without stimulation. In contrast, levels of actin or cyclin D1 remained unchanged.

Article Snippet: Gene expression profiles were generated using Applied Biosystems Mouse Genome Survey Microarray.

Techniques: Expressing, Microarray, Stable Transfection, Mutagenesis, Western Blot, Functional Assay

Journal: PLoS ONE

Article Title: Estradiol Activates β-Catenin Dependent Transcription in Neurons

doi: 10.1371/journal.pone.0005153

Figure Lengend Snippet: Results of the Microarray analysis of gene transcription.

Article Snippet: Gene expression from the two stable cell types ( A and B ) was then analyzed using the Applied Biosystems Mouse Genome Survey Microarray ( Applied Biosystems ).

Techniques: Microarray, Derivative Assay, Binding Assay, Sequencing

Journal: PLoS ONE

Article Title: Estradiol Activates β-Catenin Dependent Transcription in Neurons

doi: 10.1371/journal.pone.0005153

Figure Lengend Snippet: (A)- Gene expression profile in cDNA/N2a-m and Δ56LEF-1/N2a-m stables cell lines. The upper panel reflects the gene induction of some selected genes, in microarray analysis of RNA collected after a 45 min exposure to estradiol or Wnt3a to detect the early response. Data is expressed as log 2 R from cDNA/N2a-m cells, that we denoted as group A, and Δ56LEF-1/N2a-m cells, that we denoted as group B. The effect of the treatment was compared between the two stable cell lines (A vs B) (see “ ” for a more complete list of the annotated genes). As seen, in the panel we selected some “putative Wnt-regulated genes”, such as Tcf3 , Ccnd1 (cyclin D1), GSK3b , Myc and LEF-1 , to give some examples of the results in our arrays. We detected changes at the protein level only in Plg , although there were several genes whose expression varied. For example, the levels of plasminogen RNA were much higher in group B than group A (ratio AvsB≥1), and the expression of LEF-1 was higher in Δ56LEF-1 due to the mutant expression (ratio AvsB≤−1). The western blots below are verifications of these differences at the protein level. Among other proteins that did not change between the groups of cells were GSK3 β or myc (see western blots on the right). MMP-2 was tested although it did not display a change in its RNA levels and there was no difference in the total cell extracts. Interestingly, when conditioned medium was prepared, more pro-active MMP-2 (and less active protein) was seen in Δ56LEF-1 cells. [Gene_Symbol: Plg (plasminogen), Tcf3 , Ccnd1 (cyclin D1), GSK3b , Myc and LEF1 ]. (B)- Estradiol induction of N-cadherin and cyclin D2 may be affected by expression of the Δ56LEF-1 protein. Total cell extracts from cDNA/N2a-m cells (group A) and Δ56LEF-1/N2a-m cells (group B) were collected 24 h after estradiol or Wnt3a treatment to analyze several known Wnt or estrogen target genes. As seen in western blots, estradiol upregulated E-cadherin, N-cadherin and cyclin D2 expression in group A cells. N-cadherin and cyclin D2 were also upregulated by Wnt in group A cells. In contrast, E-cadherin expression was not Wnt responsive. The regulatory effects of estradiol on E-cadherin, N-cadherin and cyclin D2 expression were lost when Δ56LEF-1 is expressed, as seen in group B cells. In the case of E-cadherin, the loss of functional LEF-1, which acts as a known gene repressor, implies higher protein levels even without stimulation. In contrast, levels of actin or cyclin D1 remained unchanged.

Article Snippet: Gene expression from the two stable cell types ( A and B ) was then analyzed using the Applied Biosystems Mouse Genome Survey Microarray ( Applied Biosystems ).

Techniques: Expressing, Microarray, Stable Transfection, Mutagenesis, Western Blot, Functional Assay

Journal: Data in Brief

Article Title: Gene expression profile data of the developing small intestine of Id2 -deficient mice

doi: 10.1016/j.dib.2019.103717

Figure Lengend Snippet: Specifications table

Article Snippet: How data was acquired , Applied Biosystems Mouse Genome Survey Microarray Ver2.0.

Techniques: Expressing, Microarray